How many CO2’s can the host deliver to photosynthesis SU per 1 C-mol of fixed carbon? The host will use this carbon to generate ATP to energize the CO2-concentrating mechanisms that deliver CO2 to the photosynthesis SU.

Now remove feeding

##### VARY NITROGEN
# RUN USING WASTED CARBON AND NO JCO2A OR JCO2P
time <- seq(1,1230,1)
defpars <- def_pars()
env <- init_env(time=time, L=c(15,15,2), N=c(1e-7,1e-6,2), X=c(0,0,0))
run <- run_coral_wC(time=time, env=env,
                 pars=replace(defpars, 
                              c("kNPQ", "kROS", "k", "b", "sigmaCS", "sigmaCH", "jCO2a", "jCO2p"), 
                              c(40,       30,    1,   5,      0.9,         0.9, 0, 0)),
                 NPQ="fixed2")
plot_run_wC(run)

# RUN USING JCO2A (original version of model)
run <- run_coral(time=time, env=env,
                 pars=replace(defpars, 
                              c("kNPQ", "kROS", "k", "b", "sigmaCS", "sigmaCH", "jCO2a"), 
                              c(40,       30,    1,   5,      0.9,         0.9, 0.32)),
                 NPQ="fixed2")
plot_run(run)

##### VARY LIGHT
# RUN USING WASTED CARBON AND NO JCO2A OR JCO2P
time <- seq(1,1230,1)
env <- init_env(time=time, L=c(10,25,2), N=c(1e-7,1e-7,2), X=c(0,0,0))
run <- run_coral_wC(time=time, env=env,
                 pars=replace(defpars, 
                              c("kNPQ", "kROS", "k", "b", "sigmaCS", "sigmaCH", "jCO2a", "jCO2p"), 
                              c(40,       30,    1,   5,      0.9,         0.9, 0, 0)),
                 NPQ="fixed2")
plot_run_wC(run)

# RUN USING JCO2A (original version of model)
run <- run_coral(time=time, env=env,
                 pars=replace(defpars, 
                              c("kNPQ", "kROS", "k", "b", "sigmaCS", "sigmaCH", "jCO2a"), 
                              c(40,       30,    1,   5,      0.9,         0.9, 0.32)),
                 NPQ="fixed2")
plot_run(run)

Now make jPNQ inhibited

##### VARY NITROGEN
# RUN USING WASTED CARBON AND NO JCO2A OR JCO2P
time <- seq(1,1230,1)
defpars <- def_pars()
env <- init_env(time=time, L=c(15,15,2), N=c(1e-7,1e-6,2), X=c(0,0,0))
run <- run_coral_wC(time=time, env=env,
                 pars=replace(defpars, 
                              c("kNPQ", "kROS", "k", "b", "sigmaCS", "sigmaCH", "jCO2a", "jCO2p"), 
                              c(60,       40,    1,   5,      0.9,         0.9, 0, 0)),
                 NPQ="inhibited2")
plot_run_wC(run)

# RUN USING JCO2A (original version of model)
run <- run_coral(time=time, env=env,
                 pars=replace(defpars, 
                              c("kNPQ", "kROS", "k", "b", "sigmaCS", "sigmaCH", "jCO2a"), 
                              c(60,       40,    1,   5,      0.9,         0.9, 0.32)),
                 NPQ="inhibited2")
plot_run(run)

##### VARY LIGHT
# RUN USING WASTED CARBON AND NO JCO2A OR JCO2P
time <- seq(1,1230,1)
env <- init_env(time=time, L=c(10,25,2), N=c(1e-7,1e-7,2), X=c(0,0,0))
run <- run_coral_wC(time=time, env=env,
                 pars=replace(defpars, 
                              c("kNPQ", "kROS", "k", "b", "sigmaCS", "sigmaCH", "jCO2a", "jCO2p"), 
                              c(60,       40,    1,   5,      0.9,         0.9, 0, 0)),
                 NPQ="inhibited2")
plot_run_wC(run)

# RUN USING JCO2A (original version of model)
run <- run_coral(time=time, env=env,
                 pars=replace(defpars, 
                              c("kNPQ", "kROS", "k", "b", "sigmaCS", "sigmaCH", "jCO2a"), 
                              c(60,       40,    1,   5,      0.9,         0.9, 0.32)),
                 NPQ="inhibited2")
plot_run(run)

Trying different stress parameter sets

##### VARY LIGHT
# RUN USING WASTED CARBON AND NO JCO2A OR JCO2P
time <- seq(1,1230,0.5)
env <- init_env(time=time, L=c(10,40,2), N=c(1e-7,1e-7,2), X=c(0,0,0))
run <- run_coral_wC(time=time, env=env,
                 pars=replace(defpars, 
                              c("kNPQ", "kROS", "k", "b", "sigmaCS", "sigmaCH", "jCO2a", "jCO2p"), 
                              c(80,       40,    1,   5,      0.9,         0.9, 0, 0)),
                 NPQ="fixed2")
plot_run_wC(run)

run <- run_coral_wC(time=time, env=env,
                 pars=replace(defpars, 
                              c("kNPQ", "kROS", "k", "b", "sigmaCS", "sigmaCH", "jCO2a", "jCO2p"), 
                              c(80,       80,    1,   5,      0.9,         0.9, 0, 0)),
                 NPQ="fixed2")
plot_run_wC(run)

run <- run_coral_wC(time=time, env=env,
                 pars=replace(defpars, 
                              c("kNPQ", "kROS", "k", "b", "sigmaCS", "sigmaCH", "jCO2a", "jCO2p"), 
                              c(60,       60,    1,   5,      0.9,         0.9, 0, 0)),
                 NPQ="inhibited2")
plot_run_wC(run)

with(run, {
  plot(time, 5*H$jCw)
})